This series is currently '''active'''. (How to respond/input, for example if you want to suggest a molecule that should be made, is described in the [http://opensourcemalaria.org/ Landing Page] under "Join the Team")

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[https://github.com/OpenSourceMalaria/OSM_To_Do_List/issues?labels=Series+4&milestone=&page=1&state=open Automatically updated list of to do items in this Series]

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[https://github.com/OpenSourceMalaria/OSM_To_Do_List/issues?labels=Being+Synthesised+Now%2CSeries+4&page=1&state=open Automatically updated list of compounds being made in this series]

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[http://malaria.ourexperiment.org/osddmalaria_meeting_/10142 Most recent online meeting relevant to this series]

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April 2014 PDF newsletter may be downloaded using [http://malaria.ourexperiment.org/data/files/10840/OSM%20Newsletter%20April%202014.pdf this link]. Late 2014 newsletter under construction at GHI [https://github.com/OpenSourceMalaria/OSM_To_Do_List/issues/269 269].

==Introduction==

==Introduction==

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===Preamble===

===Preamble===

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The Triazolopyrazine series is the newest of the OSM series. It was announced on September 10th 2013 as Series 4.

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The Triazolopyrazine Series is the newest of the OSM series. It was announced by [http://www.mmv.org/newsroom/news/potential-new-class-antimalarials-now-open-source MMV] and on the OSM blog (''via'' [http://malaria.ourexperiment.org/osdd_malaria_shared/7949/A_New_Triazolopyrazine_Series_for_OSM__Series_4.html the briefing document] and as [http://malaria.ourexperiment.org/the_osm_blog/7954/Announcing_OSM_Series_4__the_Triazolopyrazines.html a general description]) on September 10th 2013 and is sometimes referred to as the ''TP Series'', or ''OSM Series 4''.

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The series arises from industrial work that cannot be fully disclosed which was followed by some hit-to-lead work funded directly by MMV which can.

There is evidence from parasite ion regulation assays (below) that these compounds may be PfATP4 inhibitors. Such evidence distinguishes Series 4 from Series 1-3 where there was no experimental evidence for a mechanism of action.

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The series arises from industrial work that cannot be fully disclosed which was followed by some hit-to-lead work funded directly by MMV and performed by a CRO which can.

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A great deal of exploration of the series has been done, with significant diversity in the core and pendant groups. The series includes many potent compounds, all of which are detailed on this page.

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This part of OSM is a lead optimisation project, now aiming to improve solubility, potency and metabolic stability while reducing hERG activity.

As with everything involved in OSM, suggestions can be given in [http://opensourcemalaria.org/# multiple ways].

As with everything involved in OSM, suggestions can be given in [http://opensourcemalaria.org/# multiple ways].

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===What is Known at the Start of the Campaign===

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===Start of the Campaign===

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A [http://malaria.ourexperiment.org/uri/404# briefing document] written for MMV constitutes what was known at the start of the open project.

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A [http://malaria.ourexperiment.org/uri/404# briefing document] written for MMV was the initial knowledgebase. This was accompanied by a [http://malaria.ourexperiment.org/uri/406 PDF summary of pharmacokinetics and efficacy]. This is being folded into the sections below, then supplemented.

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The authors made the following '''summary''' of their work on the triazolopyrazine series:

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"''We have made compounds in this series down to 16nM potency. The series also seems to have good in vitro HLM and hHEP stability Clint < 8.1 is compatible with 10nM potency. However, RLM remains stubbornly high, particularly for the more potent analogues translating to short half-lives in rat PK. The series also appears to have little polypharmacology or cytotoxicity. The project has so far not challenged the hypothesis that rat metabolism may not be a great model for human metabolism for this series.''"

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The aim of the campaign at the outset was to improve the metabolic stability and the pharmacokinetic properties of this series in rat so as to meet the once-dosing criteria (TCP1) set by MMV. New chemistry directed towards blocking the putative metabolic sites was a major part of the research prior to the data being contributed to OSM.

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The authors also flagged some '''concerns''' regarding the series:

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==Sources of Data on the TP Series==

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"''Although [http://en.wikipedia.org/wiki/Dofetilide# dofetilide] binding looks weak or nil, the series has shown activity in a patch clamp assay at Essen (1-10uM) which is quite potent though with a window of >100 fold over Pfal potency. The series shows activity in Kieran Kirk’s PfATP4 assay which goes away for Pfal inactives in the series. In Kip Guy’s resistant mutants the picture is perhaps more mixed, but there is still support for the idea that some members of the series are weaker in the resistant strains. The series has no or weak >>1uM activity against gametocytes, no activity against Winzeler’s Pb liver stage and may have weak activity against ookinetes but the dose-response data has not been completed."''

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[http://malaria.ourexperiment.org/biological_data/10041 Compounds Inherited from MMV] including structures and potencies ([http://malaria.ourexperiment.org/osdd_malaria_shared/8106/MMV_triazolopyrazine_data.html

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older version of this file])<br>

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[http://malaria.ourexperiment.org/uri/404# Initial briefing document] (A minor error in the briefing document referring to the amides has been [http://malaria.ourexperiment.org/uri/42d clarified].) Briefing document mostly folded into the below.<br>

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[http://malaria.ourexperiment.org/uri/406 PDF summary of pharmacokinetics and efficacy]. Needs folding into the below.<br>

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[http://malaria.ourexperiment.org/triazolopyrazine_se The current synthetic lab notebook]<br>

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[http://malaria.ourexperiment.org/osdd_malaria_shared/8292/Collected_Amides_in_the_TP_Series_Triazolopyrazines_Series_4.html Summary of Data on Amides in the Series]<br>

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[http://malaria.ourexperiment.org/data/files/7384/FINAL%20REPORT%20MMV670652.doc Document from CRO describing synthetic chemistry of some members of series]<br>

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[http://malaria.ourexperiment.org/osdd_malaria_shared/8585 The ELN post containing the raw Chemdraw and picture files for this wiki page] - if you generate new pictures, add to the ELN page.<br>

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[http://malaria.ourexperiment.org/osdd_malaria_shared/11335 Project reports by Devon Scott and Eduvie Omene, University of Edinburgh]

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Possible '''next steps''' were also suggested for the triazolopyrazine series:

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==Current Aims==

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"''The series has good potency and" in vivo "efficacy with few toxicity concerns. The biggest issue is metabolic stability, as measured in rat in particular. Some possible future directions include:

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1. Lead optimisation, to improve solubility and metabolic stability while maintaining potency and reducing hERG activity.<br>

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2. Validation of PfATP4 activity as mechanism of action.<br>

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''''* Small scale changes around the side chains to attempt to balance potency and metabolism.

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===Current/Recent Activity===

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* Incorporation of a basic centre to increase volume as a potential fix for half-life. However, this might come at the expense of plasma concentration so would require high potency. In addition of the 29 compounds with a basic centre only one has a measured potency < 100nM.

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*More significant structural changes. Of the changes made to the basic skeleton, the most successful might be the recent evaluation of the substitution position changes (eg MMV670945), possibly in combination with modifying the disposition of the N atoms in the core. Related compounds have been made by others and it would be wise to incorporate the learnings from these series into any plans to explore this substitution pattern further. The first few compounds look similar in terms of metabolic stability.''''

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The series has good potency and in vivo efficacy with few toxicity concerns. The biggest issue is metabolic stability, as measured in rat in particular. Some possible future directions include:

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Last updated: July 3rd 2014

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* Small scale changes around the side chains, particularly phenethyl to attempt to balance potency and metabolism

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(1. N is tolerated in the ring, hasn’t been explored much recently. 2. Is 3,4-diF the best substitution pattern? 3. Some evidence (eg MMV669848) that the phenethyl side chain can be rigidified, perhaps the iso-indoline of that compound could be improved on with other ring systems and by more optimal substitution of the aromatic benzene ring of the isoindoline. 4. The amide MMV670944 is interesting and shows good RLM stability, but many other amides failed to match its potency.

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* Incorporation of a basic centre to increase volume as a potential fix for half-life. However, this might come at the expense of plasma concentration so would require high potency. In addition of the 29 compounds with a basic centre only one has a measured potency < 100nM.

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* More significant structural changes. Of the changes made to the basic skeleton, the most successful might be the recent evaluation of the substitution position changes (eg MMV670945), possibly in combination with modifying the disposition of the N atoms in the core. Related compounds have been made by others and it would be wise to incorporate the learnings from these series into any plans to explore this substitution pattern further. The first few compounds look similar in terms of metabolic stability.''''

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More contents will gradually become part of this wiki (below) as the project progresses.

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1. '''Which compounds to make next?''' - see [http://malaria.ourexperiment.org/osddmalaria_meeting_/10142 the most recent meeting] for links to the discussions on these points. Compounds in the [http://malaria.ourexperiment.org/the_osm_blog/9211 ether] and [http://malaria.ourexperiment.org/the_osm_blog/9519 amide] sub-series are being made. [https://github.com/OpenSourceMalaria/OSM_To_Do_List/issues?labels=Being+Synthesised+Now&page=1&state=open Automatically-updated list of compounds being made now] - some compounds may be from older series.

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The raw data behind the briefing document will be released when it is obtained. New ion regulation assay data has already been received (below).

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2. '''Does anyone possess compounds that could be relevant to this series already?''' It [http://cdsouthan.blogspot.se/2013/12/searching-triazolopyrazines-for-open.html currently appears] as though the answer is "no".

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===What Can the Community Do Now?===

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3. '''Resources needed''': a) Chemists to make molecules, b) Experienced medicinal chemists to digest the data on this wiki and suggest new compounds to make to improve the pharmacokinetic parameters above. You can contact the OSM Consortium in many ways (go to the "Join the Team" page [http://opensourcemalaria.org/ here].

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Those wishing to contribute to OSM Series 4 should in the first instance read the [http://malaria.ourexperiment.org/uri/404# briefing document]. The first question is: Which 10 compounds ought to be made in Sept/Oct 2013 for evaluation?

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==Notable Points about Series 4==

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Resources Needed: Chemists to either make new molecules, or help obtain existing compounds that might be relevant to this series.

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* Compounds in this series have been identified down to 16 nM potency.

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* Seems to have good ''in vitro'' HLM and hHEP stability CL<sub>int</sub> < 8.1 is compatible with 10 nM potency.

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* RLM remains stubbornly high, particularly for the more potent analogues translating to short half-lives in rat PK. It's possible that rat metabolism may not be a good model for human metabolism for this series.

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* Series appears to have little polypharmacology or cytotoxicity.

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* There is strong correlation between activity ''vs.'' Pfal and activity in Kiaran Kirk’s ion regulation assay, implying the mechanism of action is inhibition of PfATP4.

* Although [http://en.wikipedia.org/wiki/Dofetilide# dofetilide] binding looks weak or nil, the series has shown activity in a patch clamp assay at Essen (1-10 μM) which is quite potent though with a window of >100 fold over Pfal potency.

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2. Validation of PfATP4 activity.<br>

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* In Kip Guy’s resistant mutants the picture is mixed, but there is still support for the idea that some members of the series are weaker in the resistant strains. The series has no or weak >>1 μM activity against gametocytes, no activity against Winzeler’s Pb liver stage and may have weak activity against ookinetes but the dose-response data has not been completed.

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===Current Questions for the Community===

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==Project Strands of Current Interest==

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Starting-point questions are listed at the end of the [http://malaria.ourexperiment.org/uri/404# briefing document]. These translate into the initial question of '''Which 10 compounds ought to be made first?''' (also asked [https://github.com/OpenSourceMalaria/OSM_To_Do_List/issues/86 here] and '''Does anyone possess compounds that could be relevant to this series already?''' (asked [https://github.com/OpenSourceMalaria/OSM_To_Do_List/issues/87 here] and there is a separate section for results below).

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The biggest issue is metabolic stability, as measured in rat in particular. There are few toxicity concerns. Thus possible future directions:

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* Small scale changes around the side chains, particularly phenethyl to attempt to balance solubility, potency and metabolism. Other possibilities: a) N is tolerated in the pendant rings, but hasn’t been explored much recently. b) Is 3,4-diF the best substitution pattern? c) Some evidence (eg MMV669848) that the phenethyl side chain can be rigidified, perhaps the iso-indoline of that compound could be improved on with other ring systems and by more optimal substitution of the aromatic benzene ring of the isoindoline. d) The amide [http://malaria.ourexperiment.org/osm_procedures/9557/Preparation_of_OSMS175.html%20OSM-S-175 MMV670944] is interesting and shows good RLM stability, but many other amides failed to match its potency.

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* Incorporation of a basic centre to increase volume as a potential fix for half-life. However, this might come at the expense of plasma concentration so would require high potency. Of the 29 compounds with a basic centre only one (MMV670437, below) has a measured potency < 100 nM (actually 44 nM).

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==Prior Knowledge of the Series==

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[[Image:MMV670437.png|thumb|center|200px|MMV670437]]

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===Potency of Hits and Analogs===

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* More significant structural changes. Of the changes made to the basic skeleton, the most successful might be the recent evaluation of the substitution position changes (''e.g.,'' MMV670945), ''possibly'' in combination with modifying the disposition of the N atoms in the core (though the triazolopyrazine has shown the best data, below).

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(Detail will be placed here, but for the moment please browse the [http://malaria.ourexperiment.org/uri/404# briefing document]).

To assess modification of the triazole part of the core, two compounds based on imadazopyrazines were made (MMV669846 and MMV670250). Both showed reduced potency against PfNF54 ''vs.'' the corresponding parent compound MMV639565. The RLM stability of MMV670250 was found to be poor.

As most of the analogs arising from core modifications were >1 μM potency, fewer were tested in RLM (though quite a few were tested in HLM). Of the 4 tested in RLM, the greatest stability had a Clint of 109, (HLM 9.5), several had HLM Clint 8 or less, particularly after moving or removing the N from the pyrazine ring. ''(<--need to locate primary data, since this disagrees with what is in the pictures here - MHT)''

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===Modification of Pyrazine Substitution Pattern===

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It was thought possible that the pyrazine moiety of the triazolopyrazine could undergo aldehyde oxidase-mediated metabolism at positions ''alpha-'' to the nitrogen. Four variations were made to the substitution of the "southernmost" (8-) ring C-H, all lowering potency ''vs.'' PfNF54.

Side chain transposition was investigated. The side-chain on the pyrazine ring was shifted to the adjacent carbon. The chain length was varied (n= 0,1,2) and linked through either O or N. Among the ethers, the phenethyl ether MMV670945 showed good potency (Pfal IC50 34 nM) but a poor stability in RLM (Cl 100 mL/min/Kg).

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[[Image:Pyrazine Transposition.png|thumb|center|950px|Transposition of the Pyrazine Side Chain and Comparisons with Closely Related Compounds]]

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===Modification of the Triazole Substitution===

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Attempts at lowering the lipophilicity of the compounds by replacing the triazole aryl substituent with a cyclo(hetero)aliphatic group, linked either by the heteroatom or otherwise (e.g. piperidine, tetrahydropyran, indoline or isoindoline) lowered the potency against PfNF54, as did an aniline substituent. A dimethylpyrazole substituent was also deleterious - note the comparison with MMV670944, which is potent.

[http://malaria.ourexperiment.org/uri/406 One of the original inherited documents] for Series 4 indicated that "heteroaryl" was not tolerated in this position, but the data do not currently support this as a blanket conclusion. Pyridinyl has been found to be a poor substituent, but one inherited compound containing a substituted pyridine was active.

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[[Image:Aromatic Variants in Northeast.png|thumb|center|600px|Heteroaryl as the Triazole's Aromatic Substituent]]

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Where an aromatic ring has been used in this position, it appears that a para-OCF<sub>3</sub> and -OCHF<sub>2</sub> groups generate higher potency than -OCH<sub>3</sub>.

The phenethyl ether side-chain on the pyrazine ring was flagged as a metabolic hot-spot and so several strategies were adopted to mitigate this risk. Some trends:

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* Changing the length of the side-chain to anything other than 3 atoms severely lowers potency against PfNF54

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* The linker atom to the pyrazine ring is crucial (O>>C>N)

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* Heteroatoms in the side-chain lowered potency with the exception of MMV669848 (not an ether - features an isoindolino-methyl group on the pyrazine ring - see later section) although this compound had poor RLM stability.

In a separate attempt to mitigate the potential metabolism in the ethyl chain it was replaced by an aromatic group through inclusion of a phenol substituent on the pyrazine ring. Some substituted phenolates were metabolically more stable '''in vitro''' as well as ''in vivo'' in rat, although with reduced potency. (''what are the numbers?'')

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Considering that the benzylic position in the phenethyl side-chain is prone to metabolic oxidation, several compounds having mono- and di-substitution in the benzylic position were made. Di-substitution lowered the potency considerably whereas mono-substitution with OMe, OCHF<sub>2</sub>, CH<sub>2</sub>OH, NMe<sub>2</sub> groups retained good potency. Additional substitution alpha- to the ether oxygen led to complete loss of potency. The alpha-OCHF<sub>2</sub> compound MMV670652, with a p-CN-phenyl group on the triazole ring, showed better RLM stability (cLogP effect). (''what is the number?'')

A small library of amides (including the ''m''-Cl benzylamide, MMV668958) showed promising potency. However, other amides (derived from aliphatic or anilines) either showed lower potency or were inactive. The RLM of MMV668958 was poor - perhaps due to benzylic oxidation. Alpha-substitution at the benzylic position or constraining the benzylamine into an aminoindane did not improve potency. Several attempts to make aniline-amides with improved potency against Pfal failed. Loading the aniline ring with lipophilic substituents marginally improved potency but led to poor RLM stability.

The ''p''-Cl benzanilide MMV670246, although not active against PfNF54, showed good RLM stability perhaps due to lack of benzylic metabolism. However, its rat PK showed high clearance. The potent ''m''-Cl (MMV669542) analog had poor RLM stability.

For the more recent set, solubility was still seen as low and needs improving. The metabolic stability measured for the recent set appears not to be a mouse-specific event and needs to be improved to deliver a candidate. Met ID data (below) could help in the design of new analogs with improved stability. Is there a correlation between metabolic stability and Log D?

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The PK curve for the relatively weak amide MMV670246 is shown below for oral & IV legs & parameters. The original data are contained in [http://openwetware.org/wiki/Image:MMV670246_rat_PK_data.png this picture].

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[[Image:MMV670246_rat_PK.png|centre|MMV670246 in rat PK|thumb|400px]]

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A compound with better ''in vitro'' balance is MMV670652 but this compound has not been in rat PK. It may be possible to improve potency by synthesis of the more potent enantiomer - this is being addressed through synthesis of the synthetically simpler methyl analog [http://malaria.ourexperiment.org/osm_procedures/9907/OSMS208.html OSM-S-208], the enantioenriched version of which was MMV669844.

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The data for MMV639565 were contained in an inherited [http://malaria.ourexperiment.org/uri/406 PDF summary of pharmacokinetics and efficacy].

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As would be expected HLM ''vs.'' RLM shows a general correlation with approx 4-fold shift on average. However, for most of the more potent analogs, this increases to over 10-fold. The figure below shows the 4 sub 30 nM compounds with HLM & RLM measured: MMV670652, MMV670945, MMV670438 and MMV670947. (''It looks like there are several other compounds here exhibiting good metabolic parameters for which we do not have data'')

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[[Image:HLM_vs_RLM.png|thumb|400px|HLM vs RLM|centre]]

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===Metabolism ID===

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MMV669844, MMV669848 and MMV670936 were [http://malaria.ourexperiment.org/uri/457 sent] for ID of metabolites and [http://malaria.ourexperiment.org/uri/49a data were obtained].

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[[Image:Compounds sent for MetID.png|thumb|center|600px|Compounds Evaluated for Metabolic ID]]

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The data suggest that the core heterocyclic ring is subjected to an oxidation (though it is not clear the extent to which the compound is oxidized, only that certain peaks are present). The nature of the side chain appeared to have little influence on the results, suggesting alteration of the side chain is probably not the way to stop turnover, meaning it is likely that amides made in this series in the near future will also suffer from this problem. Nevertheless the efficacy was seen as sufficiently promising that amides remain attractive as they are. i.e. they are sufficiently robust for this point in the project. Residual question: what is the mechanism of the clearance (oxidation)? Is it CYP mediated? Open action item [https://github.com/OpenSourceMalaria/OSM_To_Do_List/issues/124 here]. One possible route of metabolism is Aldehyde Oxidase, discussed in the next section.

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===Aldehyde Oxidase Assay===

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The possibility that the compounds were cleared by aldehyde oxidase was discussed (GHI [https://github.com/OpenSourceMalaria/OSM_To_Do_List/issues/214 214]), [http://malaria.ourexperiment.org/biological_data/10586 compounds were sent to Pfizer] for evaluation and [http://malaria.ourexperiment.org/biological_data/11208 data returned] from Scott Obach's laboratory (along with comments from him), summarized below, indicating that some Series 4 compounds were substrates for AO, and others are not.

The following five compounds were evaluated in parasite ion regulation assays in the [http://biology.anu.edu.au/kiaran_kirk/ Kirk Laboratory]; the hypothesis is that PfATP4 is a Na<sup>+</sup> ATPase that exports Na<sup>+</sup> and imports H<sup>+</sup> (or equivalent) and that the effects of the compounds on Na<sup>+</sup> concentration and pH are attributable to inhibition of this activity. Structures, potency, metabolism/solubility and raw PfATP4 assay data are [http://malaria.ourexperiment.org/biological_data/7934/ here].

The following five compounds were evaluated in parasite ion regulation assays in the [http://biology.anu.edu.au/kiaran_kirk/ Kirk Laboratory]; the hypothesis is that PfATP4 is a Na<sup>+</sup> ATPase that exports Na<sup>+</sup> and imports H<sup>+</sup> (or equivalent) and that the effects of the compounds on Na<sup>+</sup> concentration and pH are attributable to inhibition of this activity. Structures, potency, metabolism/solubility and raw PfATP4 assay data are [http://malaria.ourexperiment.org/biological_data/7934/ here].

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(i.e. note the correlation: compound inactive in these assays is the inactive analog in the plasmodium screen)

(i.e. note the correlation: compound inactive in these assays is the inactive analog in the plasmodium screen)

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==Other Sources of Compounds in this Series==

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Testing was carried out vs. PfATP4-resistant mutants ([http://malaria.ourexperiment.org/biological_data/10943 ELN entry] and GHI [https://github.com/OpenSourceMalaria/OSM_To_Do_List/issues/251 251]) in the laboratories of Kiaran Kirk and David Fidock.

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([https://github.com/OpenSourceMalaria/OSM_To_Do_List/issues/87 Community Request])

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==hERG Activity==

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MMV669844 and MMV670944 ([http://malaria.ourexperiment.org/osm_procedures/9557/Preparation_of_OSMS175.html OSM-S-175]) were evaluated in a hERG assay, with [http://malaria.ourexperiment.org/biological_data/9562 the data] indicating issues with both compounds that will need to be addressed. To investigate whether this is a problem for the series, several compounds (inherited and new, attempting to reduce cLogP - GH Issue [https://github.com/OpenSourceMalaria/OSM_To_Do_List/issues/211 #211]) [http://malaria.ourexperiment.org/biological_data/10078/Screening_of_hERG_Activity_in_Series_4_Compounds.html were evaluated for activity by AstraZeneca] using [http://dx.doi.org/10.1016/j.vascn.2006.02.003 this assay] to see if this activity can be reduced. The results suggest that either the pendant OCHF<sub>2</sub> or the amide is a problem. In contrast the [http://malaria.ourexperiment.org/biological_data/9562 previous two data points] suggest that hERG activity can be obtained with compounds containing neither feature. Future analogs will need to address this. Cumulative data shown below (from [http://malaria.ourexperiment.org/biological_data/11081 here]).

Former OSM postdoc Murray Robertson is applying literature hERG pharmacophore models to the series (GH Issue [https://github.com/OpenSourceMalaria/OSM_To_Do_List/issues/188 #188]), and a community appeal is active for a laboratory willing to run higher-throughput binding assays (GH Issue [https://github.com/OpenSourceMalaria/OSM_To_Do_List/issues/192 #192]). There is a lot of literature on hERG models (i.e. how to reduce hERG activity) with the most recent being an [http://pubs.acs.org/doi/abs/10.1021/ci400308z analysis of the ChEMBL database] concluding that the dominant influence remains lipophilicity.

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==Toxicity==

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Toxicity has been evaluated at various points for this series and has generally been found to be low. e.g. [http://malaria.ourexperiment.org/biological_data/11081 here]

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==Synthetic Chemistry==

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===Synthetic Design===

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The approach to the synthesis of Series 4 up has mainly involved the functionalization of a pyrazine core, followed by a cyclization reaction to give the triazolopyrazine which may then be subsequently functionalized. The two main series, [http://malaria.ourexperiment.org/the_osm_blog/8028 ether- and amide-linked compounds] are shown below along with a specific example of a potent compound in each series.

[http://malaria.ourexperiment.org/triazolopyrazine_se/8217 The cyclisation was achieved], initially not in the ca. 50% yields reported by the original CRO. [http://malaria.ourexperiment.org/the_osm_blog/8894 Jo Ubels] has solved this, with input from others such as a student working with Patrick Thomson, [http://malaria.ourexperiment.org/triazolopyrazine_se/8335 Devon Scott].

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The union of the alcohol fragment with the chloro-intermediate was for a long time not proceeding cleanly, and this [http://malaria.ourexperiment.org/data/files/9856/CRO%20Synth%20Series%204.doc was also found] by the CRO that first reported this route. Jo Ubels' [http://malaria.ourexperiment.org/the_osm_blog/9357 lit survey] found conditions involving a crown ether that has worked reliably. There have been periodic discussions about which alcohols to employ in the resulting synthetic scheme ([http://malaria.ourexperiment.org/the_osm_blog/9601Blog post from April 2014], GHI[https://github.com/OpenSourceMalaria/OSM_To_Do_List/issues/174 174]).

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A synthetic challenge was the efficiency of the oxidative cyclization to form the triazolopyrazine. There was much discussion of the use of oxidants such as PIDA and chloramine T (Overview GHI [https://github.com/OpenSourceMalaria/OSM_To_Do_List/issues/206 206]) as well as the possibility that hydrazone isomers were cyclising at different rates (both Github Issue [https://github.com/OpenSourceMalaria/OSM_To_Do_List/issues/97 97]).

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Some of the ether compounds contain a stereogenic centre in the benzylic position - structures are in the SAR section above, and the syntheses of these are dealt with below in the section of stereochemistry.

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===Synthesis of the Amide-Linked Series===

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'''Route 1: Initial Amide Bond Formation:'''

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It was decided (GHI[https://github.com/OpenSourceMalaria/OSM_To_Do_List/issues/121 121], GHI[https://github.com/OpenSourceMalaria/OSM_To_Do_List/issues/101 101]) to pursue a route involving initial amide bond formation with the chloro-pyrazine acid shown below ([http://malaria.ourexperiment.org/osm_procedures/8991/Preparation_of_OSMS150.html OSM-S-150]). This molecule is commercially available but is expensive, but there are now routes to it in the lab. [http://downwithmalariaupwithopensource.blogspot.co.uk/2013/10/direction-and-strategy-for-bsc-projects.html Patrick] and [https://github.com/OpenSourceMalaria/OSM_To_Do_List/issues/150 Inga] planned this synthesis and then [http://malaria.ourexperiment.org/triazolopyrazine_se/9147 Inga completed] it, as has [http://malaria.ourexperiment.org/triazolopyrazine_se/8899 Eduvie using the same approach] (data missing in the lab notebook, but [http://malaria.ourexperiment.org/osdd_malaria_shared/11335 reports are available). [http://malaria.ourexperiment.org/triazolopyrazine_se/9189 Tom scaled up] the Patrick/Eduvie/Inga approach and has been completed on a [https://github.com/OpenSourceMalaria/OSM_To_Do_List/issues/164 15 g scale] in four steps: [http://malaria.ourexperiment.org/triazolopyrazine_se/9552/post.html 1] [http://malaria.ourexperiment.org/triazolopyrazine_se/9577/post.html 2] [http://malaria.ourexperiment.org/triazolopyrazine_se/9717/post.html 3] [http://malaria.ourexperiment.org/triazolopyrazine_se/9973/post.html 4]. An assessment of the relative costs of synthesis ''vs.'' purchase was discussed (GHI[https://github.com/OpenSourceMalaria/OSM_To_Do_List/issues/163 163], GHI[https://github.com/OpenSourceMalaria/OSM_To_Do_List/issues/164 164]) but not properly completed.

Sabin has [https://github.com/OpenSourceMalaria/OSM_To_Do_List/issues/146 successfully demonstrated] an elegant alternative route to the starting pyrazine acid in one step from the methyl precursor ([http://malaria.ourexperiment.org/triazolopyrazine_se/8929 data]).

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For the subsequent coupling of the pyrazine acid with an amine, Tom and Alice have identified reliable conditions [http://malaria.ourexperiment.org/triazolopyrazine_se/9142 for the amide coupling] using T3P that worked much better than [http://malaria.ourexperiment.org/triazolopyrazine_se/8937 an attempt to go ''via'' the acid chloride]. There was an analysis of commercially-available [http://malaria.ourexperiment.org/osm_logos_and_templ/8578 primary] and [http://malaria.ourexperiment.org/the_osm_blog/8936 secondary] amines that could be employed, the [https://github.com/OpenSourceMalaria/OSM_To_Do_List/issues/123 likely physical properties of the resulting compounds] as well as an analysis of [https://github.com/OpenSourceMalaria/OSM_To_Do_List/issues/151 those amines available locally].

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Hydrazone synthesis [http://malaria.ourexperiment.org/the_osm_blog/9169 was surveyed by Inga]) and is working reliably. (Discussion about making hydrazone first, then coupling with pyrazine: GHI[https://github.com/OpenSourceMalaria/OSM_To_Do_List/issues/152 152]) Following work by Jo Ubels on optimizing the cyclization step for the ether series (above), hypervalent iodide PIDA may now be used to form the triazolopyrazine, [http://malaria.ourexperiment.org/triazolopyrazine_se/10183/post.html as in this example.]

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'''Route 2: Carbonylation'''

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An efficient alternative synthetic approach would be to use the same chloro-triazolopyrazine core as for the ether series (above) and invent a new carbonylation method to introduce the amide as the final sequence (GHI[https://github.com/OpenSourceMalaria/OSM_To_Do_List/issues/101 101], GHI[https://github.com/OpenSourceMalaria/OSM_To_Do_List/issues/126 126], [http://malaria.ourexperiment.org/the_osm_blog/8627 Inga's lit survey], [http://malaria.ourexperiment.org/the_osm_blog/8480 Alice's original appeal for a collaborator], a [http://malaria.ourexperiment.org/the_osm_blog/8173 summary of the associated discussion], Alice's framing of the relevant reactions (GHI[https://github.com/OpenSourceMalaria/OSM_To_Do_List/issues/205 205]) and [http://malaria.ourexperiment.org/the_osm_blog/10000 Tom's lit survey]. The most recent results (GHI[https://github.com/OpenSourceMalaria/OSM_To_Do_List/issues/259 259]) indicate there is a significant competing S<sub>N</sub>Ar reaction when an alcohol was used as a nucleophile. The most recent reaction to date in this series was in [http://malaria.ourexperiment.org/triazolopyrazine_se/11100 Sept 2014].

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===Alternative Routes to the Triazolopyrazine Core===

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A route permitting more late-stage diversification of the core would involve synthesis of a halogenated core that could be subjected to cross-coupling or nucleophilic displacement. Two such routes are shown below.

Preliminary progress towards both has been made by Tom Macdonald (link to Honours thesis coming). The first steps (acid-mediated cyclizations) have been successfully carried out for Halogenation Routes [http://malaria.ourexperiment.org/triazolopyrazine_se/11112 1] and [http://malaria.ourexperiment.org/triazolopyrazine_se/11034 2]. The bromination step in Route 1 has reportedly been carried out (we lack the experimental write-up) and the halogenation in Route 2 was reportedly carried out in 58% yield ([http://malaria.ourexperiment.org/triazolopyrazine_se/11024 most recent lab book entry of presumably different attempt], [http://malaria.ourexperiment.org/triazolopyrazine_se/11287 more recent attempt by Alice]).

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===Fluoroalkene Isostere===

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Jo Ubels [http://malaria.ourexperiment.org/the_osm_blog/10443 suggested] a fluoroalkene isostere for the amide series. Jo pursued a simplified version of this chemistry with a pyridine ring in place of the pyrazine. The boronic ester (rather than the acids, which were predicted and found to be unstable, GHI[https://github.com/OpenSourceMalaria/OSM_To_Do_List/issues/250 250]) was synthesized along with the bromofluoroalkene, but the coupling of these fragments has not yet been well explored. (Link to Ubels Honours thesis coming). [http://malaria.ourexperiment.org/triazolopyrazine_se/11120 Most recent experiment in this series].

Suggestion of the study of aryl-aryl interactions, with lit: GHI [https://github.com/OpenSourceMalaria/OSM_To_Do_List/issues/232 232].

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==Chirality/Stereogenic Centres in This Series==

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'''Racemates/Resolutions:''' Frontrunner compound MMV670652 was evaluated/inherited as a racemate. There was interest in separating the enantiomers (GHI[https://github.com/OpenSourceMalaria/OSM_To_Do_List/issues/115 115], GHI[https://github.com/OpenSourceMalaria/OSM_To_Do_List/issues/111 111], GHI[https://github.com/OpenSourceMalaria/OSM_To_Do_List/issues/120 120]. However, the difluoromethyl group makes the compound slightly challenging to synthesize (GHI[https://github.com/OpenSourceMalaria/OSM_To_Do_List/issues/119 119] and [http://malaria.ourexperiment.org/the_osm_blog/8470 blog post]). It is not clear that this group is needed - there are [http://malaria.ourexperiment.org/the_osm_blog/8550 related structures that could be tried], and [http://malaria.ourexperiment.org/biological_data/9191 compounds lacking this group (and indeed the whole stereogenic centre) are still active] as shown in the scheme. MMV669844 (containing CH<sub>3</sub> rather than CHF<sub>2</sub>) was an inherited compound, and was reportedly synthesized using a Sharpless epoxidation on the precursor styrene, but there are no data on the enantiomeric excess of the product - it is shown as a single enantiomer in the original briefing document, so it is presumed (only) that the sample possessed an ''ee''. Compound [http://malaria.ourexperiment.org/osm_procedures/9907/OSMS208.html OSM-S-208] (GHI[https://github.com/OpenSourceMalaria/OSM_To_Do_List/issues/166 166]), identical to MMV669844 save that it was synthesized as a racemate, was [http://malaria.ourexperiment.org/biological_data/10252 found to be reasonably potent] and can therefore be used as a surrogate for MMV670652 for the separation of enantiomers in this series (GHI[https://github.com/OpenSourceMalaria/OSM_To_Do_List/issues/111 111]). (Note there is ongoing discussion about whether compounds differing in ee, including where the ee is not known, should have different codes (GHI[https://github.com/OpenSourceMalaria/OSM_To_Do_List/issues/172 172])).

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[[Image:Focus on benzylic ethers.png|thumb|center|500px|Known/assumed Stereochemistry in the Benzylic Ether Series]]

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''Alternatives'': The CF<sub>3</sub>-substituted compound shown has yet to be made but has a prohibitively high cLogP; however the hydroxyl-substituted compound remains of interest (GHI[https://github.com/OpenSourceMalaria/OSM_To_Do_List/issues/178 178]) and the ''des''-F analog is under investigation (GHI[https://github.com/OpenSourceMalaria/OSM_To_Do_List/issues/235 235]). MMV675948 ([http://malaria.ourexperiment.org/osm_procedures/10929/OSMS265.html OSM-S-265]) was [http://malaria.ourexperiment.org/biological_data/11216/Evaluation_of_Latest_Series_4_Analogs_in_Ether_and_Amide_Series.html found to be reasonably potent], providing another simple analog suitable for enantiomer separation. GHI[https://github.com/OpenSourceMalaria/OSM_To_Do_List/issues/236 236]). Methoxy-substitured ether analogs lacking the Ph in the side chain are under investigation (GHI[https://github.com/OpenSourceMalaria/OSM_To_Do_List/issues/238 238], GHI[https://github.com/OpenSourceMalaria/OSM_To_Do_List/issues/239 239]) though the only related inherited analog (MMV670762) is inactive.

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Generally speaking all inherited compounds should be treated as racemates unless there is reason not to.

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One approach to the synthesis of the chiral alcohol fragment needed for the racemic samples (e.g. of MMV670652) [http://malaria.ourexperiment.org/triazolopyrazine_se/8378 requires a source of cyanide].

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Another approach to enantioenriched compounds in this series is through benzylic amines, either the known compounds MMV670437, MMV670763 and MMV671651 or analogs thereof (see GHI[https://github.com/OpenSourceMalaria/OSM_To_Do_List/issues/242 242], GHI[https://github.com/OpenSourceMalaria/OSM_To_Do_List/issues/241 241] and GHI[https://github.com/OpenSourceMalaria/OSM_To_Do_List/issues/240 240] respectively. (All three inherited amines were supposedly enantioenriched).

([https://github.com/OpenSourceMalaria/OSM_To_Do_List/issues/87 Original community request])<br>

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The compound series [http://cdsouthan.blogspot.se/2013/12/searching-triazolopyrazines-for-open.html appears to be novel/unusual] (related: GHI[https://github.com/OpenSourceMalaria/OSM_To_Do_List/issues/142 142]) with little similarity to compounds in PubChem/Surechem, though Chris Southan (in the previous link) found a related compound ([https://pubchem.ncbi.nlm.nih.gov/summary/summary.cgi?cid=7118230 CID 7118230]) with [https://pubchem.ncbi.nlm.nih.gov/assay/assay.cgi?aid=504832 reported antimalarial activity], with a structure similar to those described above for modification of the triazolopyrazine core. Jo Ubels also [http://malaria.ourexperiment.org/the_osm_blog/8894/An_Introduction__Joanna.html carried out a search] and found few compounds similar to Series 4.<br>

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[https://github.com/OpenSourceMalaria/OSM_To_Do_List/issues/147 A similarity was noted] between Series 4 compounds and a compound from Novartis likely active against vivax. Paul Willis suggested the mechanism of action of the Novartis compounds was likely PI4K - data and reasoning given in [http://malaria.ourexperiment.org/triazolopyrazine_se/8912 this lab book entry]. Chris Southan [http://cdsouthan.blogspot.se/2013/12/searching-triazolopyrazines-for-open.html modelled the OSM and Novartis compounds], which provides additional evidence for a different mechanism of action.

April 2014 PDF newsletter may be downloaded using this link. Late 2014 newsletter under construction at GHI 269.

Introduction

Preamble

The Triazolopyrazine Series is the newest of the OSM series. It was announced by MMV and on the OSM blog (viathe briefing document and as a general description) on September 10th 2013 and is sometimes referred to as the TP Series, or OSM Series 4.

Representative Series 4 Compound

The series arises from industrial work that cannot be fully disclosed which was followed by some hit-to-lead work funded directly by MMV and performed by a CRO which can.

A great deal of exploration of the series has been done, with significant diversity in the core and pendant groups. The series includes many potent compounds, all of which are detailed on this page.

This part of OSM is a lead optimisation project, now aiming to improve solubility, potency and metabolic stability while reducing hERG activity.

As with everything involved in OSM, suggestions can be given in multiple ways.

The aim of the campaign at the outset was to improve the metabolic stability and the pharmacokinetic properties of this series in rat so as to meet the once-dosing criteria (TCP1) set by MMV. New chemistry directed towards blocking the putative metabolic sites was a major part of the research prior to the data being contributed to OSM.

2. Does anyone possess compounds that could be relevant to this series already? It currently appears as though the answer is "no".

3. Resources needed: a) Chemists to make molecules, b) Experienced medicinal chemists to digest the data on this wiki and suggest new compounds to make to improve the pharmacokinetic parameters above. You can contact the OSM Consortium in many ways (go to the "Join the Team" page here.

Notable Points about Series 4

Compounds in this series have been identified down to 16 nM potency.

Seems to have good in vitro HLM and hHEP stability CLint < 8.1 is compatible with 10 nM potency.

RLM remains stubbornly high, particularly for the more potent analogues translating to short half-lives in rat PK. It's possible that rat metabolism may not be a good model for human metabolism for this series.

Series appears to have little polypharmacology or cytotoxicity.

There is strong correlation between activity vs. Pfal and activity in Kiaran Kirk’s ion regulation assay, implying the mechanism of action is inhibition of PfATP4.

Concerns about the TP Series

Although dofetilide binding looks weak or nil, the series has shown activity in a patch clamp assay at Essen (1-10 μM) which is quite potent though with a window of >100 fold over Pfal potency.

In Kip Guy’s resistant mutants the picture is mixed, but there is still support for the idea that some members of the series are weaker in the resistant strains. The series has no or weak >>1 μM activity against gametocytes, no activity against Winzeler’s Pb liver stage and may have weak activity against ookinetes but the dose-response data has not been completed.

Project Strands of Current Interest

The biggest issue is metabolic stability, as measured in rat in particular. There are few toxicity concerns. Thus possible future directions:

Small scale changes around the side chains, particularly phenethyl to attempt to balance solubility, potency and metabolism. Other possibilities: a) N is tolerated in the pendant rings, but hasn’t been explored much recently. b) Is 3,4-diF the best substitution pattern? c) Some evidence (eg MMV669848) that the phenethyl side chain can be rigidified, perhaps the iso-indoline of that compound could be improved on with other ring systems and by more optimal substitution of the aromatic benzene ring of the isoindoline. d) The amide MMV670944 is interesting and shows good RLM stability, but many other amides failed to match its potency.

Incorporation of a basic centre to increase volume as a potential fix for half-life. However, this might come at the expense of plasma concentration so would require high potency. Of the 29 compounds with a basic centre only one (MMV670437, below) has a measured potency < 100 nM (actually 44 nM).

MMV670437

More significant structural changes. Of the changes made to the basic skeleton, the most successful might be the recent evaluation of the substitution position changes (e.g., MMV670945), possibly in combination with modifying the disposition of the N atoms in the core (though the triazolopyrazine has shown the best data, below).

SAR

Modification of Core Triazolopyrazine

To assess modification of the triazole part of the core, two compounds based on imadazopyrazines were made (MMV669846 and MMV670250). Both showed reduced potency against PfNF54 vs. the corresponding parent compound MMV639565. The RLM stability of MMV670250 was found to be poor.

Modification of Core Triazole

Modifications to the pyrazine part of the core were not well tolerated. Several aromatic variations were tried.

Modification of Core Pyrazine, Retaining Aromaticity

Several replacements of the aromatic ring with aliphatic rings were assayed.

Modification of Core Pyrazine, Replacing Aromatic with Aliphatic Ring

As most of the analogs arising from core modifications were >1 μM potency, fewer were tested in RLM (though quite a few were tested in HLM). Of the 4 tested in RLM, the greatest stability had a Clint of 109, (HLM 9.5), several had HLM Clint 8 or less, particularly after moving or removing the N from the pyrazine ring. (<--need to locate primary data, since this disagrees with what is in the pictures here - MHT)

Modification of Pyrazine Substitution Pattern

It was thought possible that the pyrazine moiety of the triazolopyrazine could undergo aldehyde oxidase-mediated metabolism at positions alpha- to the nitrogen. Four variations were made to the substitution of the "southernmost" (8-) ring C-H, all lowering potency vs. PfNF54.

Modification of the Triazolopyrazine's 8-position

Side chain transposition was investigated. The side-chain on the pyrazine ring was shifted to the adjacent carbon. The chain length was varied (n= 0,1,2) and linked through either O or N. Among the ethers, the phenethyl ether MMV670945 showed good potency (Pfal IC50 34 nM) but a poor stability in RLM (Cl 100 mL/min/Kg).

Transposition of the Pyrazine Side Chain and Comparisons with Closely Related Compounds

Modification of the Triazole Substitution

Attempts at lowering the lipophilicity of the compounds by replacing the triazole aryl substituent with a cyclo(hetero)aliphatic group, linked either by the heteroatom or otherwise (e.g. piperidine, tetrahydropyran, indoline or isoindoline) lowered the potency against PfNF54, as did an aniline substituent. A dimethylpyrazole substituent was also deleterious - note the comparison with MMV670944, which is potent.

Major Changes to the Triazole's Aromatic Substituent

One of the original inherited documents for Series 4 indicated that "heteroaryl" was not tolerated in this position, but the data do not currently support this as a blanket conclusion. Pyridinyl has been found to be a poor substituent, but one inherited compound containing a substituted pyridine was active.

Heteroaryl as the Triazole's Aromatic Substituent

Where an aromatic ring has been used in this position, it appears that a para-OCF3 and -OCHF2 groups generate higher potency than -OCH3.

Sensitivity to Methoxy Substitution of the Triazole's Aromatic Substituent

Pyrazine Side Chain Modifications - Ethers

The phenethyl ether side-chain on the pyrazine ring was flagged as a metabolic hot-spot and so several strategies were adopted to mitigate this risk. Some trends:

Changing the length of the side-chain to anything other than 3 atoms severely lowers potency against PfNF54

The linker atom to the pyrazine ring is crucial (O>>C>N)

Heteroatoms in the side-chain lowered potency with the exception of MMV669848 (not an ether - features an isoindolino-methyl group on the pyrazine ring - see later section) although this compound had poor RLM stability.

In a separate attempt to mitigate the potential metabolism in the ethyl chain it was replaced by an aromatic group through inclusion of a phenol substituent on the pyrazine ring. Some substituted phenolates were metabolically more stable in vitro as well as in vivo in rat, although with reduced potency. (what are the numbers?)

Considering that the benzylic position in the phenethyl side-chain is prone to metabolic oxidation, several compounds having mono- and di-substitution in the benzylic position were made. Di-substitution lowered the potency considerably whereas mono-substitution with OMe, OCHF2, CH2OH, NMe2 groups retained good potency. Additional substitution alpha- to the ether oxygen led to complete loss of potency. The alpha-OCHF2 compound MMV670652, with a p-CN-phenyl group on the triazole ring, showed better RLM stability (cLogP effect). (what is the number?)

Planning of ether analogs: GHI 174 and blog appeal. Planning of more analogs in July 2014: GHI 232.

Pyrazine Side Chain Modifications - Amides

A small library of amides (including the m-Cl benzylamide, MMV668958) showed promising potency. However, other amides (derived from aliphatic or anilines) either showed lower potency or were inactive. The RLM of MMV668958 was poor - perhaps due to benzylic oxidation. Alpha-substitution at the benzylic position or constraining the benzylamine into an aminoindane did not improve potency. Several attempts to make aniline-amides with improved potency against Pfal failed. Loading the aniline ring with lipophilic substituents marginally improved potency but led to poor RLM stability.

Amides Synthesised and Tested pre-OSM

The p-Cl benzanilide MMV670246, although not active against PfNF54, showed good RLM stability perhaps due to lack of benzylic metabolism. However, its rat PK showed high clearance. The potent m-Cl (MMV669542) analog had poor RLM stability.

For the more recent set, solubility was still seen as low and needs improving. The metabolic stability measured for the recent set appears not to be a mouse-specific event and needs to be improved to deliver a candidate. Met ID data (below) could help in the design of new analogs with improved stability. Is there a correlation between metabolic stability and Log D?

The PK curve for the relatively weak amide MMV670246 is shown below for oral & IV legs & parameters. The original data are contained in this picture.

MMV670246 in rat PK

A compound with better in vitro balance is MMV670652 but this compound has not been in rat PK. It may be possible to improve potency by synthesis of the more potent enantiomer - this is being addressed through synthesis of the synthetically simpler methyl analog OSM-S-208, the enantioenriched version of which was MMV669844.

As would be expected HLM vs. RLM shows a general correlation with approx 4-fold shift on average. However, for most of the more potent analogs, this increases to over 10-fold. The figure below shows the 4 sub 30 nM compounds with HLM & RLM measured: MMV670652, MMV670945, MMV670438 and MMV670947. (It looks like there are several other compounds here exhibiting good metabolic parameters for which we do not have data)

HLM vs RLM

Metabolism ID

The data suggest that the core heterocyclic ring is subjected to an oxidation (though it is not clear the extent to which the compound is oxidized, only that certain peaks are present). The nature of the side chain appeared to have little influence on the results, suggesting alteration of the side chain is probably not the way to stop turnover, meaning it is likely that amides made in this series in the near future will also suffer from this problem. Nevertheless the efficacy was seen as sufficiently promising that amides remain attractive as they are. i.e. they are sufficiently robust for this point in the project. Residual question: what is the mechanism of the clearance (oxidation)? Is it CYP mediated? Open action item here. One possible route of metabolism is Aldehyde Oxidase, discussed in the next section.

Aldehyde Oxidase Assay

The possibility that the compounds were cleared by aldehyde oxidase was discussed (GHI 214), compounds were sent to Pfizer for evaluation and data returned from Scott Obach's laboratory (along with comments from him), summarized below, indicating that some Series 4 compounds were substrates for AO, and others are not.

Aldehyde Oxidase Assay Results from Pfizer

In Vivo Efficacy

MMV639565 and MMV669844 have both demonstrated parasite clearance in vivo, providing a highly attractive feature of this series.

The following five compounds were evaluated in parasite ion regulation assays in the Kirk Laboratory; the hypothesis is that PfATP4 is a Na+ ATPase that exports Na+ and imports H+ (or equivalent) and that the effects of the compounds on Na+ concentration and pH are attributable to inhibition of this activity. Structures, potency, metabolism/solubility and raw PfATP4 assay data are here.

The Five Compounds Initially Evaluated for Possible PfATP4 Activity

MMV669000: no (potency: inactive)

MMV669304: yes (potency: 280 nM)

MMV669360: yes (potency: 356 nM)

MMV669542: yes (potency: 185 nM)

MMV669848: yes (potency: 114 nM)

MMV669000 did not dissipate the plasma membrane Na+ gradient or increase the plasma membrane pH gradient consistent with it not inhibiting PfATP4 at the concentration tested.

The other compounds dissipated the plasma membrane Na+ gradient and increased the plasma membrane pH gradient at a concentration of 2 μM, consistent with them being PfATP4 inhibitors.

(i.e. note the correlation: compound inactive in these assays is the inactive analog in the plasmodium screen)

Testing was carried out vs. PfATP4-resistant mutants (ELN entry and GHI 251) in the laboratories of Kiaran Kirk and David Fidock.

hERG Activity

MMV669844 and MMV670944 (OSM-S-175) were evaluated in a hERG assay, with the data indicating issues with both compounds that will need to be addressed. To investigate whether this is a problem for the series, several compounds (inherited and new, attempting to reduce cLogP - GH Issue #211) were evaluated for activity by AstraZeneca using this assay to see if this activity can be reduced. The results suggest that either the pendant OCHF2 or the amide is a problem. In contrast the previous two data points suggest that hERG activity can be obtained with compounds containing neither feature. Future analogs will need to address this. Cumulative data shown below (from here).

Cumulative hERG Data on Series 4 Compounds

Former OSM postdoc Murray Robertson is applying literature hERG pharmacophore models to the series (GH Issue #188), and a community appeal is active for a laboratory willing to run higher-throughput binding assays (GH Issue #192). There is a lot of literature on hERG models (i.e. how to reduce hERG activity) with the most recent being an analysis of the ChEMBL database concluding that the dominant influence remains lipophilicity.

Toxicity

Toxicity has been evaluated at various points for this series and has generally been found to be low. e.g. here

Synthetic Chemistry

Synthetic Design

The approach to the synthesis of Series 4 up has mainly involved the functionalization of a pyrazine core, followed by a cyclization reaction to give the triazolopyrazine which may then be subsequently functionalized. The two main series, ether- and amide-linked compounds are shown below along with a specific example of a potent compound in each series.

Examples of ether and amide target molecules.

Synthesis of the Ether-Linked Series

The synthesis of members of the ether series has been largely solved by Jo Ubels, as shown below.

The union of the alcohol fragment with the chloro-intermediate was for a long time not proceeding cleanly, and this was also found by the CRO that first reported this route. Jo Ubels' lit survey found conditions involving a crown ether that has worked reliably. There have been periodic discussions about which alcohols to employ in the resulting synthetic scheme (post from April 2014, GHI174).

A synthetic challenge was the efficiency of the oxidative cyclization to form the triazolopyrazine. There was much discussion of the use of oxidants such as PIDA and chloramine T (Overview GHI 206) as well as the possibility that hydrazone isomers were cyclising at different rates (both Github Issue 97).

Some of the ether compounds contain a stereogenic centre in the benzylic position - structures are in the SAR section above, and the syntheses of these are dealt with below in the section of stereochemistry.

Hydrazone synthesis was surveyed by Inga) and is working reliably. (Discussion about making hydrazone first, then coupling with pyrazine: GHI152) Following work by Jo Ubels on optimizing the cyclization step for the ether series (above), hypervalent iodide PIDA may now be used to form the triazolopyrazine, as in this example.

Alternative Routes to the Triazolopyrazine Core

A route permitting more late-stage diversification of the core would involve synthesis of a halogenated core that could be subjected to cross-coupling or nucleophilic displacement. Two such routes are shown below.

Routes to the Halogenated Core Triazolopyrazine

Preliminary progress towards both has been made by Tom Macdonald (link to Honours thesis coming). The first steps (acid-mediated cyclizations) have been successfully carried out for Halogenation Routes 1 and 2. The bromination step in Route 1 has reportedly been carried out (we lack the experimental write-up) and the halogenation in Route 2 was reportedly carried out in 58% yield (most recent lab book entry of presumably different attempt, more recent attempt by Alice).

Fluoroalkene Isostere

Jo Ubels suggested a fluoroalkene isostere for the amide series. Jo pursued a simplified version of this chemistry with a pyridine ring in place of the pyrazine. The boronic ester (rather than the acids, which were predicted and found to be unstable, GHI250) was synthesized along with the bromofluoroalkene, but the coupling of these fragments has not yet been well explored. (Link to Ubels Honours thesis coming). Most recent experiment in this series.

Route Devised to Fluoroalkene Isostere of Amide

Spectroscopy

Chirality/Stereogenic Centres in This Series

Racemates/Resolutions: Frontrunner compound MMV670652 was evaluated/inherited as a racemate. There was interest in separating the enantiomers (GHI115, GHI111, GHI120. However, the difluoromethyl group makes the compound slightly challenging to synthesize (GHI119 and blog post). It is not clear that this group is needed - there are related structures that could be tried, and compounds lacking this group (and indeed the whole stereogenic centre) are still active as shown in the scheme. MMV669844 (containing CH3 rather than CHF2) was an inherited compound, and was reportedly synthesized using a Sharpless epoxidation on the precursor styrene, but there are no data on the enantiomeric excess of the product - it is shown as a single enantiomer in the original briefing document, so it is presumed (only) that the sample possessed an ee. Compound OSM-S-208 (GHI166), identical to MMV669844 save that it was synthesized as a racemate, was found to be reasonably potent and can therefore be used as a surrogate for MMV670652 for the separation of enantiomers in this series (GHI111). (Note there is ongoing discussion about whether compounds differing in ee, including where the ee is not known, should have different codes (GHI172)).

Known/assumed Stereochemistry in the Benzylic Ether Series

Alternatives: The CF3-substituted compound shown has yet to be made but has a prohibitively high cLogP; however the hydroxyl-substituted compound remains of interest (GHI178) and the des-F analog is under investigation (GHI235). MMV675948 (OSM-S-265) was found to be reasonably potent, providing another simple analog suitable for enantiomer separation. GHI236). Methoxy-substitured ether analogs lacking the Ph in the side chain are under investigation (GHI238, GHI239) though the only related inherited analog (MMV670762) is inactive.

Generally speaking all inherited compounds should be treated as racemates unless there is reason not to.

One approach to the synthesis of the chiral alcohol fragment needed for the racemic samples (e.g. of MMV670652) requires a source of cyanide.

Another approach to enantioenriched compounds in this series is through benzylic amines, either the known compounds MMV670437, MMV670763 and MMV671651 or analogs thereof (see GHI242, GHI241 and GHI240 respectively. (All three inherited amines were supposedly enantioenriched).